Was the recall performed on the computer? I would call with the S/N of the truck to see...sounds like my issue I had, only I couldn't go above 30mph...cleared it with the scan gauge, and then brought it in.

Yes I was up to date on the recalls when I got my new tires and alignment a few months ago. Drives just fine. Just lights on and flashing.
Can't get to a code to clear it because the ultra gauge just says scanning.

Ok so I started the truck several times each time waiting after clicking aux on. Also switching in and out of 4x4. I unplugged the ultra gauge and plugged it back in with the truck running. Success, it worked. Also popped up an error code. U0155. Looking at the tundra trouble codes the number might match P0155 = O2Sensor Heater Circuit Malfunction (Bank #2 Sensor #1)

Well after restarting a few more times all the lights went off. I then cleared the code and things seem to be back in order. I will find out tomorrow.

Yea i still had it on when i pulled the battery off. I called hypertech and they said that you can keep it plugged in when disconnected a battery. Should be no issues.
Like you said, it could have been some weird signals that the truck didn't like though.